The bowfin genome illuminates the developmental evolution of ray-finned fishes

• Published in: Nature genetics Vol. 53; no. 9; pp. 1373 - 1384
• Main Authors: Thompson, Andrew W., Hawkins, M. Brent, Parey, Elise, Wcisel, Dustin J., Ota, Tatsuya, Kawasaki, Kazuhiko, Funk, Emily, Losilla, Mauricio, Fitch, Olivia E., Pan, Qiaowei, Feron, Romain, Louis, Alexandra, Montfort, Jérôme, Milhes, Marine, Racicot, Brett L., Childs, Kevin L., Fontenot, Quenton, Ferrara, Allyse, David, Solomon R., McCune, Amy R., Dornburg, Alex, Yoder, Jeffrey A., Guiguen, Yann, Roest Crollius, Hugues, Berthelot, Camille, Harris, Matthew P., Braasch, Ingo
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.09.2021; Nature Publishing Group
• Subjects: 631/136; 631/208/212; 631/601; Agriculture; Animal Genetics and Genomics; Animals; Biodiversity; Biological Evolution; Biomedical and Life Sciences; Biomedicine; Bowfins; Cancer Research; Chromatin; Chromatin - genetics; Chromosomes; Evolution; Evolution & development; Evolution, Molecular; Evolutionary genetics; Fish; Fishes; Gene expression; Gene Function; Gene regulation; Genetic aspects; Genetic research; Genome - genetics; Genomes; Genomics; Human Genetics; Life Sciences; Observations; Phenotypes; Phylogenetics; Phylogeny; Properties; Skates, Fish - genetics; Skates, Fish - immunology; Skates, Fish - physiology; Vertebrates; Whole Genome Sequencing; United States
• ISSN: 1061-4036; 1546-1718; 1546-1718
• DOI: 10.1038/s41588-021-00914-y

The bowfin ( Amia calva ) is a ray-finned fish that possesses a unique suite of ancestral and derived phenotypes, which are key to understanding vertebrate evolution. The phylogenetic position of bowfin as a representative of neopterygian fishes, its archetypical body plan and its unduplicated and slowly evolving genome make bowfin a central species for the genomic exploration of ray-finned fishes. Here we present a chromosome-level genome assembly for bowfin that enables gene-order analyses, settling long-debated neopterygian phylogenetic relationships. We examine chromatin accessibility and gene expression through bowfin development to investigate the evolution of immune, scale, respiratory and fin skeletal systems and identify hundreds of gene-regulatory loci conserved across vertebrates. These resources connect developmental evolution among bony fishes, further highlighting the bowfin’s importance for illuminating vertebrate biology and diversity in the genomic era. Analysis of a chromosome-level bowfin genome assembly sheds light into neopterygian fish evolution. Chromatin accessibility and gene expression profiling provides insight into bowfin embryonic development.